User: raf4

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raf420
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r***@cumc.columbia.edu

Posts by raf4

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve and Gordon, When the reads were aligned with the same algorithm, the glitch disappeared. Thanks and best wishes, Rich ...
written 10 weeks ago by raf420
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Comment: C: Problem running featurecounts in Rsubread on GFF file
... I believe I found part of the problem. I should  not have used the patched sequence. I am currently downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ GCA_000001405.15_GRCh38 ...
written 12 weeks ago by raf420
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Comment: C: problem running featurecounts using hg38 in-built annotation
... I believe I found the problem. I should  not have used the patched sequence. I am currently downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ GCA_000001405.15_GRCh38_no_alt_ ...
written 12 weeks ago by raf420
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problem running featurecounts using hg38 in-built annotation
... Dear List, I am having trouble running feature counts as implemented in Rsubread on my mac My script is: library(Rsubread) b1.res<-featureCounts(files="b1.res.bam",annot.inbuilt="hg38",isPairedEnd=TRUE,requireBothEndsMapped=FALSE) I get an output file with numbers instead of gene names and n ...
featurecounts hg38 written 12 weeks ago by raf420
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Comment: C: Problem running featurecounts in Rsubread on GFF file
... an addendum, It ran to completion with teh following output file" b1.res.bam NA    22698646 I will now try it with the internal annotation, but please let me know if the hg38 annotation can be applied to the patch. THANKS! Rich       ...
written 12 weeks ago by raf420
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Problem running featurecounts in Rsubread on GFF file
... Dear Bioconductor list: I have aligned some paired end reads to the human genome assembly CRCh38.p7 with R subread. I am now trying to count the reads with feature counts. It is taking over an hour on my mac, and as I recall it should run faster. This is teh first time that I have used featurecount ...
rsubread gff featurecounts grch38.p7 vs hg38 written 12 weeks ago by raf420
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Answer: A: Rsubread crash on Mac during alignment
... Dear Wei and Yang, I am sorry that I didn't get back to you. The person whom I was helping when I found the bug went elsewhere. I am curently using the new version and it works fine. Thanks and best wishes, Rich ...
written 12 weeks ago by raf420
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve and Gordon, I have since found out that the count  files were indeed produced by the sequencing core here using different alignment algorithms and different assemblies (gtf files)! I have suggested that the investigator whom I am helping ask the core to realign the older read data with the ne ...
written 3 months ago by raf420
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Comment: C: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve and Gordon, Thank you for your answers. I just remembered that the first batch was mapped to ENSEMBL and then translated to NCBI gene symbols. The second was mapped NCBI genes. That must be the problem. I will analyze them in a compatible way henceforth. If batch corrections are necessary, I ...
written 3 months ago by raf420 • updated 3 months ago by Gordon Smyth31k
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Comment: A: Subject: Strange glitch in Voom curve resulting from batch effects
... Steve, Most of the genes were the same. I forget the number of NAs but I can check. fewer than 1,000 I think. There are 5 replicates of one condition in the old batch and 5 replicates each for 4 conditions in the new batch. The filter I used for low expressing genes is: isexpr<-rowSums(cpm(y) ...
written 3 months ago by raf420 • updated 3 months ago by Gordon Smyth31k

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